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Membrane topology inversion of SecG detected by labeling with a membrane-impermeable sulfhydryl reagent that causes a close association of SecG with SecA.

SecG stimulates protein translocation in Escherichia coli by facilitating the membrane insertion-deinsertion cycle of SecA. SecG was previously shown to undergo membrane topology inversion, since SecA-dependent protein translocation renders the membrane-protected region of SecG sensitive to external proteases. To examine this topology inversion in more detail without protease-treatment, SecG derivatives with a single cysteine residue at various positions were labeled in the presence and absence of protein translocation with a membrane impermeable SH reagent, 4-acetamido-4'-maleimidylstilbene-2-2'-disulfonic acid (AMS). Treatment of spheroplasts with AMS revealed that a cysteine residue in the cytoplasmic region of SecG could be labeled from the periplasm side only in the presence of protein translocation, whereas a cytoplasmic protein, elongation factor, Tu, remained unlabeled. Treatment of inverted membrane vesicles with AMS also revealed that cysteine residues in the periplasmic region were labeled from the cytoplasmic side of membranes only when protein translocation was in progress. This labeling required ATP, SecA and a precursor protein, and became more efficient as the position of the cysteine residue became closer to the C-terminus. Crosslinking analyses revealed that the interaction between SecG and SecA in membranes markedly increases when SecA and SecG undergo membrane-insertion and topology inversion, respectively. Thus, the two most dynamic components of the translocation machinery were found for the first time to interact with each other when both undergo conformational changes.

Adenosine Triphosphatases↗

New and highly efficient method for silkworm transgenesis using Autographa californica nucleopolyhedrovirus and piggyBac transposable elements.

We have developed a new method for the transgenesis of the silkworm, Bombyx mori. This method couples the use of recombinant baculoviruses with the use of the piggyBac transposable element. One recombinant AcNPV, designated the helper virus, is designed to express the piggyBac transposase under the control of the Drosophila hsp70 promoter. Another recombinant AcNPV encoded the gene to be incorporated into the silkworm genome, in this case a green fluorescent protein (GFP) gene, under the control of B. mori actin A3 promoter and franked by the piggyBac inverted terminal repeats. Preblastoderm eggs were inoculated with a fine needle coated with a mixture of these two recombinant baculoviruses. Most of the inoculated larvae hatched and a high proportion of the newly hatched G0 larvae expressed the GFP marker. Transgenesis was confirmed by Southern blot analysis of G1 insects, sequencing the insertion site junctions isolated by inverse PCR, and the marker segregated in Mendelian fashion, as evidenced by the appearance of green fluorescence in G2 insects. Thus, transgenic silkworms were easily and efficiently obtained using this new method.

Animals↗

Genome juggling by transposons: Tam3-induced rearrangements in Antirrhinum majus.

Transposable elements are well known for their ability to generate large- and small-scale rearrangements of the sequences flanking their insertion sites. These include deletions, inversions, and duplications. Tam3, a transposon from the Snapdragon (Antirrhinum majus), is highly active in the generation of such rearrangements. We have analysed a number of Tam3-induced rearrangements at the nivea (niv) locus by Southern blotting, cloning, and sequence determination. The data obtained from these analyses have led to an understanding of the mechanisms by which these complex alleles were formed. We have shown that the primary rearrangements usually occur without excision of the element and therefore result from aberrant transposition attempts. Subsequent rearrangements may occur on excision of the element. Finally, we suggest how the analysis of such rearrangements may not only provide information about Tam3 transposition but also show how transposon-induced rearrangements may influence the structure and function of the genome as a whole.

Base Sequence↗

Instability of pUC19 in Escherichia coli transcription termination factor mutant, rho026.

The higher copy number of pUC19, compared to its parent plasmid pBR322, is known to be due to deletion of rop, also known as rom, and to an ori mutation that impedes RNAI:RNAII interaction. pUC19, unlike pBR322, fails to transform E. coli rho mutant rho026 cells. Here we identify two features of pUC19 that contribute to this transformation defect. (1) The pUCori mutation is involved because replacing the pUCori with that of pBR322 restored transformation. (2) Transcription from the lac promoter in pUC19 is important, since deletion or inversion of the promoter or insertion of a transcription terminator (lambdat0) downstream of it restored transformation. Host RNase E activity is responsible for the transformation defect because introduction of an rne-1 allele into rho026 cells suppressed this defect, indicating that RNAI instability due to RNase E is aggravated in the rho026 strain. We suggest that in rho026 cells pUC19 RNAI:RNAII interaction is more impeded than in rho+ cells and Rop/Rom may confer stability by protecting RNAI against RNase E activity because expression of a rom gene inserted into pUC19 restored transformation.

Bacterial Proteins↗

The polyvalent staphylococcal phage phi 812: its host-range mutants and related phages.

Ninety-five percent of 782 culture collection strains, as well as hospital strains of Staphylococcus aureus subsp. aureus of different provenance and 43% of 89 culture collection strains of different coagulase-negative species of the genus Staphylococcus, were found to be sensitive to the polyvalent phage phi 812 or to at least one of its host-range mutants or to the polyvalent phages SK311, phi 131, and U16. Thus sensitivity to the polyvalent staphylococcal phages seems to be one of the common features of S. aureus subsp. aureus strains. The adsorption kinetics and one-step growth characteristics of the phages phi 812 and SK311 were estimated. Restriction genomic maps of the phages phi 812 (146.5 kb) and SK311 (141.1 kb) were constructed by use of the restriction endonucleases AvaII, PstI, KpnI, SacI, SmaI, and XhoI. The host-range mutations of the phage phi 812 were localized on this map. Comparison of restriction patterns of the phages phi 812 and SK311 with those of the polyvalent phages U16 and phi 131 suggests that all these phages are closely related. Their genomes differ from each other mostly by some deletions, insertions (1-3 kb), or inversions. Evidence was given that the phage phi 812 together with SK311, phi 131, and U16 belongs in the phage species Twort, the description of which is substantially supplemented with the data on the phage phi 812 reported in this paper.

Adsorption↗

Suppression of spin diffusion in selected frequency bands of nuclear Overhauser spectra.

A variant of two-dimensional nuclear Overhauser effect spectroscopy (NOESY) is described that yields information about cross-relaxation rates between pairs of spins, while the migration of magnetization through several consecutive steps (spin diffusion via neighboring spins) is largely suppressed. This can be achieved by inserting a doubly-selective inversion pulse in a conventional NOESY sequence.

Base Sequence↗

Cytoplasmic male sterility in sunflower is correlated with the co-transcription of a new open reading frame with the atpA gene.

The organization and expression of the mitochondrial (mt) genome of fertile, male-sterile and restored lines of Helianthus annuus and of H. petiolaris were compared to identify alterations which might lead to cytoplasmic male sterility (CMS). The mtDNAs of fertile and male-sterile lines differ by an 11 kb inversion and a 5 kb insertion. The rearrangements seem to be the result of recombination events within an inverted repeat of 261 bp. Detectable alterations in the transcript pattern of the rearranged mtDNA regions are restricted to the atpA locus. The male-sterile line CMSBaso shows three additional transcripts of the atpA locus of about 2500, 1200 and 250 nucleotides which are not detectable in Baso. However, the coding sequences of the atpA gene are entirely identical in the fertile line Baso and the male-sterile line CMSBaso. But a new open reading frame (orfH522) of 522 nucleotides is co-transcribed with the atpA gene as an additional larger transcript of about 2500 nucleotides in CMSBaso. orfH522 is also included in a second additional transcript of about 1200 nucleotides. The predicted translation product of orfH522 might play a role in CMS in sunflower.

Amino Acid Sequence↗

Structure of extrachromosomal circular DNAs generated by immunoglobulin light chain gene rearrangements.

Recombination at the immunoglobulin kappa or lambda light chain locus generates extrachromosomal circular DNAs. We have isolated circular DNAs from adult mouse spleen cells and prepared a circular DNA clone library. We characterized four J kappa-positive and one J lambda 1-positive clones. The J kappa-clones contained both coding and signal joints of V kappa-J kappa joining, and the J lambda 1-clone contained a signal joint of V lambda 1-J lambda 1 joining. Genomic organization of the V kappa gene families used in these joints suggested the excision of circular DNA preceded by inversion. A specific dinucleotide (P) insertion in the coding joint was observed in two clones. Three coding joints were out of frame and one clone had an in-frame coding joint, although possibly combined with a pseudo-V kappa gene. These kappa-positive circular DNAs are possibly excised from the chromosome by secondary recombinations which replace non-productive primary rearrangements.

Amino Acid Sequence↗

Chromosomal insertions localized around oriC affect the cell cycle in Escherichia coli.

The present work reports the effects of localized insertions around the origin of Escherichia coli chromosome, oriC, on cell cycle parameters. These insertions cause an increase of the C period with an inverse correlation to the distance from oriC. In addition, Omega insertion near oriC causes an increase in the number of replication forks per chromosome, n, and Tn10 insertion causes a decrease in growth rate. We found that the same insertion positioned in another region of the chromosome, outside of oriC, has a negligible effect on the C period. Marker frequency analysis suggests a slower replication velocity along the whole chromosome. We propose that the insertions positioned at less than 2 kbp from oriC could create a structural alteration in the origin of replication that would result in a longer C period. Flow cytometry reveals that asynchrony is not associated with these alterations.

Cell Cycle↗

The transcription factor Evi-1.

Evi-1 is a transcription factor with two sets of zinc finger domains. The temporally and spatially restricted pattern of Evi-1 expression in embryonic tissues suggests a role of Evi-1 in organogenesis and morphogenesis in mouse development. Mice lacking Evi-1, which die within the first few weeks of life with multiple defects in embryonic development, suggest that Evi-1 is essential for developmental cell proliferation, vascularization, and cell-specific signaling at midgestation. In hematopoietic cells, Evi-1 expression is restricted at a transient stage of myeloid cell differentiation. Constitutive expression of Evi-1 in hematopoietic cells, which is caused by retroviral insertions or chromosomal translocations and inversions, is closely associated with myelogenous leukemias and myelodysplastic syndromes in mice and humans. In the aspect of potential therapeutic approaches, some pharmaceutical drugs or antisense oligonucleotides that repress Evi-1 expression would be useful for the treatment of Evi-1-induced neoplastic tumors.

Animals↗

The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.

The chloroplast genome of Pelargonium x hortorum has been completely sequenced. It maps as a circular molecule of 217,942 bp and is both the largest and most rearranged land plant chloroplast genome yet sequenced. It features 2 copies of a greatly expanded inverted repeat (IR) of 75,741 bp each and, consequently, diminished single-copy regions of 59,710 and 6,750 bp. Despite the increase in size and complexity of the genome, the gene content is similar to that of other angiosperms, with the exceptions of a large number of pseudogenes, the recognition of 2 open reading frames (ORF56 and ORF42) in the trnA intron with similarities to previously identified mitochondrial products (ACRS and pvs-trnA), the losses of accD and trnT-ggu and, in particular, the presence of a highly divergent set of rpoA-like ORFs rather than a single, easily recognized gene for rpoA. The 3-fold expansion of the IR (relative to most angiosperms) accounts for most of the size increase of the genome, but an additional 10% of the size increase is related to the large number of repeats found. The Pelargonium genome contains 35 times as many 31 bp or larger repeats than the unrearranged genome of Spinacia. Most of these repeats occur near the rearrangement hotspots, and 2 different associations of repeats are localized in these regions. These associations are characterized by full or partial duplications of several genes, most of which appear to be nonfunctional copies or pseudogenes. These duplications may also be linked to the disruption of at least 1 but possibly 2 or 3 operons. We propose simple models that account for the major rearrangements with a minimum of 8 IR boundary changes and 12 inversions in addition to several insertions of duplicated sequence.

Chloroplasts↗

The Maillard hypothesis on aging: time to focus on DNA.

Aging is the outcome of the contest between chemistry and biology in living systems. Chronic, cumulative chemical modifications compromise the structure and function of biomolecules throughout the body. Proteins with long life spans serve as cumulators of exposure to chemical damage, which is detectable in the form of advanced glycation and lipoxidation end products (AGEs, ALEs); amino acids modified by reactive oxygen, chlorine, and nitrogen species; and deamidated and racemized amino acids. Not all of these modifications are oxidative in nature, although oxidative reactions are an important source of age-related damage. Measurements of AGEs and ALEs in proteins are useful for assessing the rate and extent of Maillard reaction damage, but it is the damage to the genome that undoubtedly has the greatest effect on the viability of the organism. The extent of genomic damage represents a balance between the rate of modification and the rate and fidelity of repair. Damage to DNA accumulates not in the form of modified nucleic acids, but as chemically "silent" errors in repair-insertions, deletions, substitutions, transpositions, and inversions in DNA sequences-that affect the expression and structure of proteins. These mutations are random, vary from cell to cell, and are passed forward from one cell generation to another. Although they are not detectable in DNA by conventional analytical techniques, purines and pyrimidines modified by Maillard reaction intermediates may be detectable in urine, and studies on these compounds should provide insight into the role of Maillard reactions of DNA in aging and disease.

Aging↗

Genome sequence of Yersinia pestis KIM.

We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing surprising amounts of locally colinear "backbone," or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of E. coli pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.

Bacteriophages↗

Genome organization and transcription in archaebacteria.

The genome organization of the archaebacteria is investigated in three model systems: a) rRNA genes of various archaebacteria, b) a plasmid of 15.6 kb from Sulfolobus acidocaldarius which exists in free or integrated form, c) the 59 kb genome of phage phi H of Halobacterium halobium as a model for the unusual structural variability of DNA in this organism. Several variants of this phage have been isolated, their genomes differ by several insertions, a deletion, and an inversion. The frequent inversion and circularization of a 12 kb segment of DNA appears to be linked to the presence of two copies of an IS element at its flanks. DNA-dependent RNA polymerases have been isolated from a large number of archaebacteria including representatives of 4 families of the novel order Thermoproteales . As shown by immunological methods, they are closely related to those of eukaryotes. Two different types of RNA polymerase exist in the two main branches of the archaebacteria. The role of one component of the enzyme of Thermoplasma acidophilum was elucidated using an in vitro transcription system.

Archaea↗

Quantitative comparison of soft tissue-bone interface at chondral ligament insertions in the rabbit knee joint.

At chondral ligament insertions the calcified fibrocartilage interdigitates deeply with the lamellar bone. The shape of this interface is formed under physiological loading conditions. For the purpose of morphological comparison between different ligament entheses in the rabbit knee, the number and frequency of interdigitations and thickness of calcified fibrocartilage were quantitated at the femoral insertion of the medial collateral ligament, both insertions of the cruciate ligaments, and the tibial insertion of the patellar ligament. Among the insertions, the femoral insertion of the medial collateral ligament showed the lowest frequency and depth of interdigitations at the soft tissue-bone interface, but had the thickest zone of calcified fibrocartilage. An inverse relationship was found at the insertion interface of the cruciate and patellar ligaments. The frequency and depth of interdigations at the bone-soft tissue interface at different chondral entheses seem to be related to the mechanical strength of the respective ligament; meanwhile it may be hypothesised that the thickness of the calcified fibrocartilage might be more related to the amount of motion which takes place at an insertion.

Animals↗

IS50-mediated inverse transposition: specificity and precision.

The IS50 elements, which are present as inverted repeats in the kanamycin-resistance transposon, Tn5, can move in unison carrying with them any interstitial DNA segment. In consequence, DNA molecules such as a lambda::Tn5 phage genome are composed of two overlapping transposons - the kan segment bracketed by IS50 elements (Tn5), and lambda bracketed by IS50 elements. During direct transposition, mediated by IS50 "O" (outside) ends, the kan gene is moved and the lambda vector is left behind. During inverse transposition, mediated by the "I" (inside) ends of the IS50 elements, the lambda vector segment is moved and the kan gene is left behind. Direct transposition is several orders of magnitude more frequent than inverse transposition (Isberg and Syvanen, 1981; Sasakawa and Berg, 1982). We assessed the specificity and precision of the rare events mediated by pairs of I ends by mapping and sequencing independent inverse transpositions from a lambda::Tn5 phage into the amp and tet genes of plasmid pBR322. Using restriction analyses, 32 and 40 distinct sites of insertion were found among 46 and 72 independent inverse transpositions into the amp and tet genes, respectively. Eleven sites were used in two or more insertion events, and the two sites in tet used most frequently corresponded to major hotspots for the insertion of the Tn5 (by direct transposition). The sequences of 22 sites of inverse transposition (including each of the sites used more than once) were determined, in eleven cases by analyzing both pBR322-IS50 junctions, and in eleven others by sequencing one junction. The sequence of the "I" end of IS50 was preserved and 9-bp target sequence duplications were present in every case analyzed. GC pairs were found at each end of the target sequence duplication in ten of the eleven sites used more than once, and also in seven of the other eleven sites. Our data indicate that transposition mediated by pairs of "I" ends is similar in its specificity and precision to the more frequent transposition mediated by IS50 "O" ends.

Base Sequence↗

Transcriptional analysis of Ty1 deletion and inversion derivatives at CYC7.

One class of Ty insertion mutation in Saccharomyces cerevisiae activates expression of adjacent structural genes. The CYC7-H2 mutation, in which a Ty1 element is inserted 5' to the iso-2-cytochrome c coding region of CYC7, causes a 20-fold increase in CYC7 expression. Deletion analysis of CYC7-H2 has shown that distal regions of the Ty1 element are not essential for the transcriptional activation at CYC7. In this report, we have analyzed Ty1 and CYC7 RNA from two CYC7-H2 deletion derivative genes to determine whether a direct correlation exists between transcription of Ty1 and transcription of the adjacent gene. Assuming that all Ty1 elements in the genome are transcribed equally, amounts of CYC7-H2 deletion derivative Ty1 RNA were found to be at least fivefold lower than the amount estimated for the average Ty1 element. These same Ty1 deletion derivatives caused a 20-fold increase in adjacent CYC7 expression. This finding suggests that the mechanism by which Ty1 activates adjacent gene expression does not require normal levels of Ty1 transcription. Two inversion derivatives of the CYC7-H2 Ty1 have also been analyzed. These derivatives did not produce any iso-2-cytochrome c or any normal CYC7 mRNA. Instead they were found to produce a Tyl-CYC7 fusion RNA. Consistent with our findings on CYC7-H2 Ty1 transcription, the amount of the fusion RNA was very low. In addition, the Ty1 inversion derivatives produced a new RNA that mapped to sequences upstream from the inverted Ty1 segment. Similar to Ty1 insertions that activate transcription, the new RNA was found to be transcribed away from Ty1.

Alleles↗

Midline diastema and frenum morphology in the primary dentition.

PURPOSE: The purpose of this study was to determine the prevalence of different types and insertions of labial frenums as well as midline diastema in Peruvian children between 0 and 6 years of age. METHODS: A sample of 1,355 children was selected for the study. A clinical examination was done to classify the labial frenum, measure gingival insertion levels, and quantify midline diastema. Descriptive statistics and the Spearman test were used. RESULTS: The most prevalent frenums were the simple frenum (59%) and the persistent tectolabial frenum (25%). The level of gingival insertion moved apically with age. The midline diastema was wider in younger children and decreased with age. A significant inverse relationship (r=-0.27; P=.001) was found between the level of gingival insertion and the midline diastema. CONCLUSION: The most prevalent frenum was the simple frenum. A significant inverse correlation between the gingival insertion level and the midline diastema was found.

Age Factors↗